BEIRUT—An Australian reporter jailed in Egypt for more than a year was deported on Sunday, winding down a case emblematic of the crackdown that imprisoned tens of thousands of perceived opponents of President Abdel Fattah Al Sisi’s new regime after a coup.

Peter Greste was one of three imprisoned reporters from the Qatar-based Al Jazeera English language channel. There was no word on the fate of his colleagues, Canadian-Egyptian Mohamed Fahmy and Egyptian Baher Mohamed. Mr. Greste, who had served 400 days of a 7-year...